Soil nematode communities can provide valuable information about the structure and functions of soil food webs, and are sensitive to agricultural practices, including short-term straw incorporation. However, currently, such effects under long-term straw incorporation conditions at different fertility levels are largely unknown. Thus, we conducted a 13-year ongoing experiment to evaluate the effects of long-term straw incorporation on the structure and functions of the soil food web in low and high fertility soils through analyzing its effects on nematode communities, food web indices and metabolic footprints. Four treatments were included: straw removal (–S) under non-fertilized (–NPK) or fertilized (+NPK) conditions; and straw incorporation (+S) under –NPK or +NPK conditions. Soil samples from a 0–20 cm depth layer were collected when wheat and rice were harvested. Compared with straw removal, straw incorporation increased the abundances of total nematodes, bacterivores, plant-parasites and omnivores-predators, as well the relative abundances of omnivores-predators with increases of 73.06, 89.29, 95.31, 238.98, and 114.61% in –NPK soils and 16.23, 2.23, 19.01, 141.38, and 90.23% in +NPK soils, respectively. Regardless of sampling times and fertilization effects, straw incorporation increased the diversity and community stability of nematodes, as indicated by the Shannon-Weaver diversity index and maturity index. Enrichment and structure index did not show significant responses to straw incorporation, but a slight increase was observed in the structure index. The analysis of nematode metabolic footprints showed that straw incorporation increased the plant-parasite footprint and structure footprint by 97.27 and 305.39% in –NPK soils and by 11.29 and 149.56% in +NPK soils, but did not significantly influence enrichment, bacterivore and fungivore footprints. In conclusion, long-term straw incorporation, particularly under a low fertility level, favored the soil nematodes and regulated the soil food web mainly via a top-down effect.